Iron in PDB 3qu8: Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.
Enzymatic activity of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.
All present enzymatic activity of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.:
1.14.14.1;
Protein crystallography data
The structure of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine., PDB code: 3qu8
was solved by
M.B.Shah,
J.Pascual,
C.D.Stout,
J.R.Halpert,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.51 /
2.80
|
Space group
|
P 32
|
Cell size a, b, c (Å), α, β, γ (°)
|
101.880,
101.880,
299.509,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.8 /
25.9
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.
(pdb code 3qu8). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine., PDB code: 3qu8:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3qu8
Go back to
Iron Binding Sites List in 3qu8
Iron binding site 1 out
of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:36.0
occ:1.00
|
FE
|
A:HEM500
|
0.0
|
36.0
|
1.0
|
NA
|
A:HEM500
|
2.1
|
30.8
|
1.0
|
NC
|
A:HEM500
|
2.1
|
32.6
|
1.0
|
NB
|
A:HEM500
|
2.1
|
33.2
|
1.0
|
ND
|
A:HEM500
|
2.1
|
31.3
|
1.0
|
SG
|
A:CYS436
|
2.3
|
38.5
|
1.0
|
NAL
|
A:3QU501
|
2.3
|
51.6
|
1.0
|
C4C
|
A:HEM500
|
3.1
|
31.9
|
1.0
|
C1A
|
A:HEM500
|
3.1
|
30.0
|
1.0
|
C1C
|
A:HEM500
|
3.1
|
31.1
|
1.0
|
C4A
|
A:HEM500
|
3.1
|
31.4
|
1.0
|
C1D
|
A:HEM500
|
3.1
|
31.2
|
1.0
|
C4D
|
A:HEM500
|
3.1
|
30.2
|
1.0
|
C4B
|
A:HEM500
|
3.1
|
34.2
|
1.0
|
C1B
|
A:HEM500
|
3.1
|
34.3
|
1.0
|
CAC
|
A:3QU501
|
3.2
|
49.7
|
1.0
|
CAD
|
A:3QU501
|
3.2
|
52.4
|
1.0
|
CHD
|
A:HEM500
|
3.4
|
32.2
|
1.0
|
CHA
|
A:HEM500
|
3.4
|
30.7
|
1.0
|
CHC
|
A:HEM500
|
3.5
|
33.9
|
1.0
|
CHB
|
A:HEM500
|
3.5
|
31.9
|
1.0
|
CB
|
A:CYS436
|
3.5
|
38.2
|
1.0
|
CA
|
A:CYS436
|
4.1
|
38.4
|
1.0
|
C3C
|
A:HEM500
|
4.2
|
29.3
|
1.0
|
C2C
|
A:HEM500
|
4.3
|
29.3
|
1.0
|
C2A
|
A:HEM500
|
4.3
|
29.4
|
1.0
|
C3A
|
A:HEM500
|
4.3
|
29.7
|
1.0
|
C3B
|
A:HEM500
|
4.3
|
35.0
|
1.0
|
C2B
|
A:HEM500
|
4.3
|
35.6
|
1.0
|
C2D
|
A:HEM500
|
4.3
|
28.7
|
1.0
|
C3D
|
A:HEM500
|
4.3
|
30.2
|
1.0
|
CAE
|
A:3QU501
|
4.5
|
47.6
|
1.0
|
CAF
|
A:3QU501
|
4.6
|
50.7
|
1.0
|
C
|
A:CYS436
|
4.8
|
39.0
|
1.0
|
N
|
A:LEU437
|
4.9
|
39.1
|
1.0
|
N
|
A:GLY438
|
5.0
|
40.3
|
1.0
|
|
Iron binding site 2 out
of 6 in 3qu8
Go back to
Iron Binding Sites List in 3qu8
Iron binding site 2 out
of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:25.5
occ:1.00
|
FE
|
B:HEM500
|
0.0
|
25.5
|
1.0
|
NC
|
B:HEM500
|
1.9
|
19.7
|
1.0
|
NA
|
B:HEM500
|
2.0
|
17.4
|
1.0
|
NB
|
B:HEM500
|
2.0
|
20.1
|
1.0
|
ND
|
B:HEM500
|
2.1
|
18.8
|
1.0
|
SG
|
B:CYS436
|
2.2
|
38.2
|
1.0
|
NAL
|
B:3QU501
|
2.3
|
51.6
|
1.0
|
C4C
|
B:HEM500
|
2.9
|
20.9
|
1.0
|
C4A
|
B:HEM500
|
2.9
|
19.9
|
1.0
|
C1A
|
B:HEM500
|
3.0
|
19.2
|
1.0
|
C1C
|
B:HEM500
|
3.0
|
20.9
|
1.0
|
C1B
|
B:HEM500
|
3.0
|
21.6
|
1.0
|
C1D
|
B:HEM500
|
3.1
|
20.3
|
1.0
|
C4D
|
B:HEM500
|
3.1
|
19.8
|
1.0
|
CAC
|
B:3QU501
|
3.1
|
49.7
|
1.0
|
C4B
|
B:HEM500
|
3.1
|
19.9
|
1.0
|
CAD
|
B:3QU501
|
3.2
|
52.4
|
1.0
|
CHD
|
B:HEM500
|
3.3
|
22.5
|
1.0
|
CB
|
B:CYS436
|
3.4
|
37.9
|
1.0
|
CHB
|
B:HEM500
|
3.4
|
19.7
|
1.0
|
CHA
|
B:HEM500
|
3.4
|
18.9
|
1.0
|
CHC
|
B:HEM500
|
3.5
|
17.8
|
1.0
|
C3C
|
B:HEM500
|
4.1
|
21.2
|
1.0
|
C3A
|
B:HEM500
|
4.2
|
21.6
|
1.0
|
CA
|
B:CYS436
|
4.2
|
38.4
|
1.0
|
C2C
|
B:HEM500
|
4.2
|
20.3
|
1.0
|
C2A
|
B:HEM500
|
4.2
|
21.0
|
1.0
|
C2B
|
B:HEM500
|
4.3
|
20.9
|
1.0
|
C3B
|
B:HEM500
|
4.3
|
19.7
|
1.0
|
C2D
|
B:HEM500
|
4.3
|
18.7
|
1.0
|
C3D
|
B:HEM500
|
4.3
|
21.0
|
1.0
|
CAE
|
B:3QU501
|
4.4
|
47.6
|
1.0
|
CAF
|
B:3QU501
|
4.5
|
50.7
|
1.0
|
C
|
B:CYS436
|
4.9
|
38.9
|
1.0
|
CAM
|
B:3QU501
|
5.0
|
50.3
|
1.0
|
OG1
|
B:THR302
|
5.0
|
54.4
|
1.0
|
|
Iron binding site 3 out
of 6 in 3qu8
Go back to
Iron Binding Sites List in 3qu8
Iron binding site 3 out
of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe500
b:32.7
occ:1.00
|
FE
|
C:HEM500
|
0.0
|
32.7
|
1.0
|
NC
|
C:HEM500
|
1.7
|
29.8
|
1.0
|
NB
|
C:HEM500
|
1.8
|
24.9
|
1.0
|
ND
|
C:HEM500
|
1.9
|
24.4
|
1.0
|
NA
|
C:HEM500
|
1.9
|
27.1
|
1.0
|
SG
|
C:CYS436
|
2.3
|
20.0
|
1.0
|
NAL
|
C:3QU501
|
2.4
|
51.6
|
1.0
|
C4C
|
C:HEM500
|
2.7
|
27.9
|
1.0
|
C1D
|
C:HEM500
|
2.8
|
26.9
|
1.0
|
C1C
|
C:HEM500
|
2.8
|
30.5
|
1.0
|
C4B
|
C:HEM500
|
2.8
|
25.7
|
1.0
|
C1B
|
C:HEM500
|
2.8
|
26.9
|
1.0
|
C4A
|
C:HEM500
|
2.9
|
28.6
|
1.0
|
C1A
|
C:HEM500
|
3.0
|
27.6
|
1.0
|
C4D
|
C:HEM500
|
3.1
|
24.0
|
1.0
|
CHD
|
C:HEM500
|
3.1
|
28.0
|
1.0
|
CB
|
C:CYS436
|
3.2
|
20.0
|
1.0
|
CAC
|
C:3QU501
|
3.2
|
49.7
|
1.0
|
CAD
|
C:3QU501
|
3.2
|
52.4
|
1.0
|
CHC
|
C:HEM500
|
3.3
|
29.2
|
1.0
|
CHB
|
C:HEM500
|
3.3
|
26.0
|
1.0
|
CHA
|
C:HEM500
|
3.5
|
27.1
|
1.0
|
C3C
|
C:HEM500
|
3.9
|
28.6
|
1.0
|
C2C
|
C:HEM500
|
4.0
|
27.3
|
1.0
|
C3B
|
C:HEM500
|
4.0
|
24.4
|
1.0
|
C2B
|
C:HEM500
|
4.0
|
26.3
|
1.0
|
C2D
|
C:HEM500
|
4.1
|
25.6
|
1.0
|
CA
|
C:CYS436
|
4.1
|
30.0
|
1.0
|
C3A
|
C:HEM500
|
4.2
|
28.9
|
1.0
|
C2A
|
C:HEM500
|
4.2
|
28.6
|
1.0
|
C3D
|
C:HEM500
|
4.2
|
23.3
|
1.0
|
CAE
|
C:3QU501
|
4.6
|
47.6
|
1.0
|
CAF
|
C:3QU501
|
4.6
|
50.7
|
1.0
|
C
|
C:CYS436
|
4.8
|
30.0
|
1.0
|
N
|
C:GLY438
|
5.0
|
39.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 3qu8
Go back to
Iron Binding Sites List in 3qu8
Iron binding site 4 out
of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe500
b:36.2
occ:1.00
|
FE
|
D:HEM500
|
0.0
|
36.2
|
1.0
|
NA
|
D:HEM500
|
2.1
|
33.2
|
1.0
|
NC
|
D:HEM500
|
2.1
|
35.6
|
1.0
|
NB
|
D:HEM500
|
2.1
|
32.9
|
1.0
|
ND
|
D:HEM500
|
2.1
|
29.9
|
1.0
|
SG
|
D:CYS436
|
2.3
|
38.5
|
1.0
|
NAL
|
D:3QU501
|
2.3
|
49.7
|
1.0
|
C1A
|
D:HEM500
|
3.1
|
33.1
|
1.0
|
C4C
|
D:HEM500
|
3.1
|
35.3
|
1.0
|
C1C
|
D:HEM500
|
3.1
|
38.9
|
1.0
|
C4A
|
D:HEM500
|
3.1
|
34.0
|
1.0
|
C4D
|
D:HEM500
|
3.1
|
29.7
|
1.0
|
C1D
|
D:HEM500
|
3.1
|
32.3
|
1.0
|
C4B
|
D:HEM500
|
3.1
|
36.9
|
1.0
|
C1B
|
D:HEM500
|
3.1
|
33.1
|
1.0
|
CAC
|
D:3QU501
|
3.2
|
49.7
|
1.0
|
CAD
|
D:3QU501
|
3.2
|
47.9
|
1.0
|
CB
|
D:CYS436
|
3.2
|
38.1
|
1.0
|
CHA
|
D:HEM500
|
3.4
|
33.5
|
1.0
|
CHD
|
D:HEM500
|
3.4
|
31.6
|
1.0
|
CHC
|
D:HEM500
|
3.5
|
39.3
|
1.0
|
CHB
|
D:HEM500
|
3.5
|
32.9
|
1.0
|
CA
|
D:CYS436
|
4.1
|
38.3
|
1.0
|
C3C
|
D:HEM500
|
4.3
|
37.9
|
1.0
|
C2C
|
D:HEM500
|
4.3
|
38.9
|
1.0
|
C2A
|
D:HEM500
|
4.3
|
32.1
|
1.0
|
C3A
|
D:HEM500
|
4.3
|
34.0
|
1.0
|
C3B
|
D:HEM500
|
4.3
|
35.0
|
1.0
|
C2B
|
D:HEM500
|
4.3
|
32.2
|
1.0
|
C3D
|
D:HEM500
|
4.3
|
27.9
|
1.0
|
C2D
|
D:HEM500
|
4.3
|
32.1
|
1.0
|
CAE
|
D:3QU501
|
4.5
|
49.7
|
1.0
|
CAF
|
D:3QU501
|
4.5
|
49.0
|
1.0
|
C
|
D:CYS436
|
4.8
|
39.1
|
1.0
|
N
|
D:GLY438
|
4.9
|
40.1
|
1.0
|
|
Iron binding site 5 out
of 6 in 3qu8
Go back to
Iron Binding Sites List in 3qu8
Iron binding site 5 out
of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe500
b:35.1
occ:1.00
|
FE
|
E:HEM500
|
0.0
|
35.1
|
1.0
|
NA
|
E:HEM500
|
2.1
|
25.5
|
1.0
|
NC
|
E:HEM500
|
2.1
|
30.2
|
1.0
|
NB
|
E:HEM500
|
2.1
|
29.1
|
1.0
|
ND
|
E:HEM500
|
2.1
|
27.2
|
1.0
|
NAL
|
E:3QU501
|
2.3
|
57.2
|
1.0
|
SG
|
E:CYS436
|
2.3
|
38.9
|
1.0
|
CAC
|
E:3QU501
|
3.0
|
55.5
|
1.0
|
C4C
|
E:HEM500
|
3.1
|
30.9
|
1.0
|
C1A
|
E:HEM500
|
3.1
|
28.2
|
1.0
|
C1C
|
E:HEM500
|
3.1
|
32.3
|
1.0
|
C4A
|
E:HEM500
|
3.1
|
28.1
|
1.0
|
C4D
|
E:HEM500
|
3.1
|
26.2
|
1.0
|
C1D
|
E:HEM500
|
3.1
|
25.7
|
1.0
|
C4B
|
E:HEM500
|
3.1
|
30.8
|
1.0
|
C1B
|
E:HEM500
|
3.1
|
32.0
|
1.0
|
CAD
|
E:3QU501
|
3.3
|
57.5
|
1.0
|
CB
|
E:CYS436
|
3.4
|
38.0
|
1.0
|
CHA
|
E:HEM500
|
3.4
|
24.3
|
1.0
|
CHD
|
E:HEM500
|
3.4
|
26.7
|
1.0
|
CHC
|
E:HEM500
|
3.5
|
30.5
|
1.0
|
CHB
|
E:HEM500
|
3.5
|
32.7
|
1.0
|
CA
|
E:CYS436
|
4.2
|
38.3
|
1.0
|
C3C
|
E:HEM500
|
4.2
|
30.8
|
1.0
|
C2C
|
E:HEM500
|
4.3
|
32.5
|
1.0
|
C2A
|
E:HEM500
|
4.3
|
27.9
|
1.0
|
C3A
|
E:HEM500
|
4.3
|
27.4
|
1.0
|
C3B
|
E:HEM500
|
4.3
|
33.2
|
1.0
|
C2B
|
E:HEM500
|
4.3
|
32.2
|
1.0
|
C3D
|
E:HEM500
|
4.3
|
25.9
|
1.0
|
C2D
|
E:HEM500
|
4.3
|
25.5
|
1.0
|
CAE
|
E:3QU501
|
4.3
|
55.6
|
1.0
|
CAF
|
E:3QU501
|
4.6
|
59.0
|
1.0
|
C
|
E:CYS436
|
4.8
|
38.8
|
1.0
|
CAM
|
E:3QU501
|
5.0
|
57.7
|
1.0
|
|
Iron binding site 6 out
of 6 in 3qu8
Go back to
Iron Binding Sites List in 3qu8
Iron binding site 6 out
of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe500
b:61.1
occ:1.00
|
FE
|
F:HEM500
|
0.0
|
61.1
|
1.0
|
NC
|
F:HEM500
|
2.1
|
63.5
|
1.0
|
NA
|
F:HEM500
|
2.1
|
63.5
|
1.0
|
NB
|
F:HEM500
|
2.1
|
64.4
|
1.0
|
ND
|
F:HEM500
|
2.1
|
64.0
|
1.0
|
SG
|
F:CYS436
|
2.2
|
41.2
|
1.0
|
C4C
|
F:HEM500
|
3.1
|
64.7
|
1.0
|
C1A
|
F:HEM500
|
3.1
|
63.4
|
1.0
|
C4A
|
F:HEM500
|
3.1
|
65.4
|
1.0
|
C1C
|
F:HEM500
|
3.1
|
64.8
|
1.0
|
C1D
|
F:HEM500
|
3.1
|
64.8
|
1.0
|
C4D
|
F:HEM500
|
3.1
|
65.1
|
1.0
|
C1B
|
F:HEM500
|
3.1
|
66.1
|
1.0
|
C4B
|
F:HEM500
|
3.1
|
65.9
|
1.0
|
CB
|
F:CYS436
|
3.4
|
38.2
|
1.0
|
CHD
|
F:HEM500
|
3.4
|
65.7
|
1.0
|
CHA
|
F:HEM500
|
3.4
|
63.6
|
1.0
|
CHB
|
F:HEM500
|
3.5
|
65.8
|
1.0
|
CHC
|
F:HEM500
|
3.5
|
65.6
|
1.0
|
CA
|
F:CYS436
|
4.1
|
38.5
|
1.0
|
C2A
|
F:HEM500
|
4.3
|
64.0
|
1.0
|
C3C
|
F:HEM500
|
4.3
|
65.2
|
1.0
|
C3A
|
F:HEM500
|
4.3
|
66.2
|
1.0
|
C2C
|
F:HEM500
|
4.3
|
65.9
|
1.0
|
C3B
|
F:HEM500
|
4.3
|
65.9
|
1.0
|
C2B
|
F:HEM500
|
4.3
|
66.8
|
1.0
|
C2D
|
F:HEM500
|
4.3
|
65.6
|
1.0
|
C3D
|
F:HEM500
|
4.3
|
65.7
|
1.0
|
C
|
F:CYS436
|
4.8
|
39.2
|
1.0
|
CB
|
F:ALA298
|
4.9
|
48.0
|
1.0
|
N
|
F:GLY438
|
4.9
|
40.3
|
1.0
|
N
|
F:LEU437
|
4.9
|
39.1
|
1.0
|
|
Reference:
M.B.Shah,
J.Pascual,
Q.Zhang,
C.D.Stout,
J.R.Halpert.
Structures of Cytochrome P450 2B6 Bound to 4-Benzylpyridine and 4-(4-Nitrobenzyl)Pyridine: Insight Into Inhibitor Binding and Rearrangement of Active Site Side Chains. Mol.Pharmacol. V. 80 1047 2011.
ISSN: ISSN 0026-895X
PubMed: 21875942
DOI: 10.1124/MOL.111.074427
Page generated: Sun Aug 4 18:54:28 2024
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